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It’s wretched weather for putting out to sea: gusty winds, cloud banks brooding with rain and water spouts, temperatures a micro-notch above freezing and the waters of Tokyo Bay like wet elephant hide. Nonetheless, at the generous invitation of the Tokyo Metropolitan Government’s Bureau of Port and Harbor, I’ve come to the Takeshiba Terminal to enjoy a free “minicruise” of the Port of Tokyo on board a 31-meter vessel, the Shin Tokyo Maru. As I slip over the ship’s gangplank, I can’t help but hum the theme song to “Gilligan’s Island,” the iconic TV sitcom that all began with the fateful trip of the tiny ship S.S. Minnow.

Luckily, the Shin Tokyo Maru is no such small fry. The gleaming white three-deck cruiser is immaculate, given that it was first launched in 1983, and, inside at least, appears set to receive the executive board of the United Nations. A vast conference table dominates the first deck, surrounded by 30 office chairs in lace antimacassars. The second deck, too, is appointed like a formal living room, with standing lamps, coffee tables and a box chandelier that tinkles with each shift of the boat’s hull. Only the faint odor of marine fuel in the air and the revving of engines clue me in that the voyage has begun.

Pausing to admire photos of Emperor Akihito and Empress Michiko, who toured on board back in 1983, I head up to the third deck. Special members of the media are allowed up here, where the captain and his engineers work throttles to ease the craft from its dock. It seems unwise to crowd the crew, however, so I head to a door at the rear of the control deck, which leads outdoors.

Here, I face howling winds and stinging rain. I’m joined by a skeletal TV crew, also guests. The ship’s nautical glass is too thick to shoot through, so those of us charged with getting images exchange grimaces of professional misery as the Shin Tokyo Maru navigates toward Rainbow Bridge. However, being on the bay offers excellent 360-degree displays of weather. Gossamer curtains of rain drape the sky and I happily observe that we are headed toward a dramatic bar of sunshine behind a squadron of gantry cranes lined up at Shinagawa.

Before cruising under Rainbow Bridge, we pass Tokyo Port’s oldest terminal, the Hinode Pier, which was constructed in 1925 and is currently frequented by the Sumida River water buses as well as various restaurant cruise boats. To the left, we pass Harumi Terminal, designed to host passenger cruise ships, and then, to the right, at the base of Rainbow Bridge, Shibaura Terminal, which handles primarily paper and cement shipments.

As we approach Shinagawa Terminal, red and orange gantry cranes, like giraffes in rugby sweatshirts, signal that we’re nearing the heavy business end of the port. Shinagawa Terminal handles Hokkaido-Tokyo liners and container vessels on Asian routes. Battling in the wind to read the handy pamphlet distributed to cruise guests, I learn the terminal also hosts RORO ships, or “roll-on/roll-off” vessels that are used to carry wheeled cargo. I face the wind and attempt to get the song “Row, Row, Row Your Boat,” out of my head.

Passing between the next two container terminals, Oi and Aomi, I begin to get a sense of the scale that makes Keihin Ports — which include Tokyo, Kawasaki and Yokohama — the 17th largest terminal in the world, according to the World Shipping Council’s 2013 figures. And, with future growth in mind, the metropolitan government has a “berth plan.” Renovations are scheduled for many of the 204 berths, and additional ones will be built by 2027.

Finally veering east, the Shin Tokyo Maru navigates past an area enclosed like a giant swimming pool. Rain pelts down once again, and I take refuge in the bridge, which is warm and weatherproof, and now full of weather refugees. Over a loudspeaker, a guide explains that we are passing the Outer Central Breakwater Reclamation Area. It’s divided into three parts: The western section is reclaimed land comprised of dredging materials; the eastern portion is waste ash, unburnable garbage, sludge and sewage; and the part that looks like the swimming pool is the New Waste Disposal Area. There are plans to extend this out a bit further — just to the edge of the shipping lanes — but once these final blocks are filled, Tokyo Port will have run out of area to fill.

“That won’t happen anytime soon,” Tomoharu Nishihira, 47-year-old director of public relations for the Bureau of Port and Harbor, assures me. I raise an eyebrow. “We have space left yet, and techniques for processing waste are getting more sophisticated,” says Nishihara. I hope he’s right.

We approach the dynamic truss cantilever structure of Tokyo Gate Bridge, which I catch as the ship’s windshield wipers swish panes clear. We glide past the lumber-handling basins at Shin Kiba, and the loudspeaker guide turns our attention to the Inner Central Breakwater Reclamation Area. This is the sight of Umi no Mori (Sea Forest), a reforestation project chaired by architect Tadao Ando.

The 88-hectare landfill is meant to be transformed into a woodlands to cool winds before they enter central Tokyo, battling some of the city’s fierce summer heat issues. Approximately 50 hectares are to be planted and opened to the public in the fiscal year starting 2016, and the park will host various Olympic events in 2020, including eventing cross-country, rowing, canoe sprint and mountain biking.

With a perfectly orchestrated docking at Aomi Terminal, the tour for the day ends and guests disembark. Because I’ve made special arrangements in advance, I stay on board the Shin Tokyo Maru as it propels home to Hamarikyu Gardens. To navigate the waterway entrance, barely wide enough for our craft, Capt. Seiichi Kyogoku, 66, and his crew are on high alert, calling out clearance in centimeters on either side. With 45 years of boating experience behind him, Kyogoku is brave and sure, but also wise enough to take nothing for granted.

Once back on terra firma, I salute the crew a fond farewell. Nishihira, his sea-worthy public relations colleague and I then grab a cab, headed for Shinagawa’s container yards. I’ve requested a peek at how the Port of Tokyo’s daily average of 236,000 tons of cargo is handled. I mumble something about how cool it would be to watch operations from the control cabin of a gantry crane. Nishihira shakes his head; the crane is a no-go. In fact, due to international laws and clearance issues, no one’s permitted to do that and simply being allowed near the area requires special permission. “It’s my first time seeing operations from the freight yard, too,” Nishihira admits.

When I meet 50-year-old Toshiyuki Sato, deputy general manager of the Shinagawa branch of Daiichi Transportation and Terminal Co., he intuits almost instantly what I hope to see. We climb to the roof of the container center and we all soak in the activity on the wharf, a ballet of contradictions. Massive, gritty machinery moves in a “Swan Lake” of cables, containers and carriers. Skilled operators of straddle carriers — like premiers danseurs — pick out, lift and delicately puzzle into place boxes that weigh in the vicinity of 30 tons each.

I watch enraptured until a new front of rain threatens. Sato, underlining the rigors of this stage, informs me that the wharf is in motion 24 hours a day, every day of the year, except New Year’s Day. When you’re handling an annual 86 million tons of imported and exported goods, I guess there’s no sitting by the dock of the bay.

Thanking Sato for his precious time, Nishihara, his colleague and I scurry off in the freezing rain. Hoping to buy a warm drink before heading home, we stop in at what appears to be a Lawson convenience store, but which goes by the name “Port Store.” Ducking inside, it appears to have the usual Lawson fare, with the exception of heavy-grade rubber gloves, wool watch caps, hand warmers and, ahem, an inordinate number of soft-porn magazines. Oh well, I muse, any Port Store in a storm.

Tokyo Metropolitan Government’s Bureau of Port and Harbor holds occasional free tours. Check Twitter (@tocho_kouwan) and Facebook (Port.of.Tokyo.Japan) for upcoming times and dates.

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